LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -46.879902 0.0000000) to (33.149097 46.879902 4.0498067) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9476264 4.5480502 4.0498067 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -46.879902 0.0000000) to (33.149097 46.879902 4.0498067) create_atoms CPU = 0.002 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9476264 4.5480502 4.0498067 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -46.879902 0.0000000) to (33.149097 46.879902 4.0498067) create_atoms CPU = 0.001 seconds 538 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 29 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1072 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_179420363944_001#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.001 | 5.001 | 5.001 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3846.2183 0 -3846.2183 104733.14 81 0 -4584.9063 0 -4584.9063 4972.5623 Loop time of 12.3933 on 1 procs for 81 steps with 1072 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3846.21831411936 -4584.90174900028 -4584.90633292713 Force two-norm initial, final = 1075.9660 0.21725608 Force max component initial, final = 294.79896 0.034513522 Final line search alpha, max atom move = 1.0000000 0.034513522 Iterations, force evaluations = 81 144 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.362 | 12.362 | 12.362 | 0.0 | 99.75 Neigh | 0.013499 | 0.013499 | 0.013499 | 0.0 | 0.11 Comm | 0.0095412 | 0.0095412 | 0.0095412 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008562 | | | 0.07 Nlocal: 1072.00 ave 1072 max 1072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5720.00 ave 5720 max 5720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117456.0 ave 117456 max 117456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117456 Ave neighs/atom = 109.56716 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.995 | 4.995 | 4.995 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -4584.9063 0 -4584.9063 4972.5623 12587.013 87 0 -4585.1893 0 -4585.1893 -47.332615 12623.171 Loop time of 0.68298 on 1 procs for 6 steps with 1072 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4584.90633292712 -4585.18677235639 -4585.18928270599 Force two-norm initial, final = 106.99282 0.74591991 Force max component initial, final = 106.73549 0.52043846 Final line search alpha, max atom move = 0.00014484974 7.5385375e-05 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.67971 | 0.67971 | 0.67971 | 0.0 | 99.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00041565 | 0.00041565 | 0.00041565 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002853 | | | 0.42 Nlocal: 1072.00 ave 1072 max 1072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5728.00 ave 5728 max 5728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117704.0 ave 117704 max 117704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117704 Ave neighs/atom = 109.79851 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.133 | 5.133 | 5.133 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4585.1893 0 -4585.1893 -47.332615 Loop time of 2.261e-06 on 1 procs for 0 steps with 1072 atoms 176.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.261e-06 | | |100.00 Nlocal: 1072.00 ave 1072 max 1072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5728.00 ave 5728 max 5728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117424.0 ave 117424 max 117424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117424 Ave neighs/atom = 109.53731 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.133 | 5.133 | 5.133 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -4585.1893 -4585.1893 33.115489 94.273751 4.0433981 -47.332615 -47.332615 -22.412291 -53.634235 -65.951319 2.275003 459.47239 Loop time of 2.354e-06 on 1 procs for 0 steps with 1072 atoms 212.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.354e-06 | | |100.00 Nlocal: 1072.00 ave 1072 max 1072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5728.00 ave 5728 max 5728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58712.0 ave 58712 max 58712 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117424.0 ave 117424 max 117424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117424 Ave neighs/atom = 109.53731 Neighbor list builds = 0 Dangerous builds = 0 1072 -4585.18928270599 eV 2.27500298350877 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13